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Supplementary Figure 1. Somatic mutations detected in histiocytic neoplasms. Supplementary Figure 2. Frequencies of known activating kinase mutations in histiocytic neoplasms. Supplementary Figure 3. ARAF mutations and variants of unknown significance detected in BRAFV600E-wildtype, non-Langerhans Cell Histiocytic neoplasms. Supplementary Figure 4. Clinical and histological images of the non-Langerhans cell histiocytosis (non-LCH) lesions from index patients with kinase fusions identified by RNA-seq. Supplementary Figure 5. Gene expression analysis of histiocytic neoplasms by RNA-seq. Supplementary Table 1. Characteristics of patient samples with histiocytic neoplasms used in this study and genomic analysis utilized for each sample. Supplementary Table 2. Whole exome sequencing metrics. Supplementary Table 3. Somatic variants identified by whole exome and whole transcriptome sequencing and validated by droplet-digital PCR and/or custom-capture targeted next-generation sequencing with variant allele frequencies (VAFs). Supplementary Table 4. List of the top 1% of differentially expressed genes across histiocytic samples from mRNA sequencing. Supplementary Table 5. PCR primers with M13F2 and M13R2 tails (blue) for Sanger sequencing used in the targeted sequencing recurrence testing for MAP2K1 exons 2 and 3 and all coding regions of ARAF.

Supplementary Figures S1-S12

Although mutations in the gene encoding the RNA splicing factor SF3B1 are frequent in multiple cancers, their functional effects and therapeutic dependencies are poorly understood. Here, we characterize 98 tumors and 12 isogenic cell lines harboring SF3B1 hotspot mutations, identifying hundreds of cryptic 3′ splice sites common and specific to different cancer types. Regulatory network analysis revealed that the most common SF3B1 mutation activates MYC via effects conserved across human and mouse cells. SF3B1 mutations promote decay of transcripts encoding the protein phosphatase 2A (PP2A) subunit PPP2R5A, increasing MYC S62 and BCL2 S70 phosphorylation which, in turn, promotes MYC protein stability and impair apoptosis, respectively. Genetic PPP2R5A restoration or pharmacologic PP2A activation impaired SF3B1-mutant tumorigenesis, elucidating a therapeutic approach to aberrant splicing by mutant SF3B1.Significance:Here, we identify that mutations in SF3B1, the most commonly mutated splicing factor gene across cancers, alter splicing of a specific subunit of the PP2A serine/threonine phosphatase complex to confer post-translational MYC and BCL2 activation, which is therapeutically intervenable using an FDA-approved drug.See related commentary by O'Connor and Narla, p. 765.This article is highlighted in the In This Issue feature, p. 747

Supplementary Figure S1-S13 and Figure captions and Supplementary methods

Number and frequency of XPO1 hotspot mutations found across cancer types.

Fold-change in abundance and statistical significance of proteins in XPO1E571K/WT versus XPO1WT NALM-6 cells detected by SILAC analysis of nuclear fractions

Fold-change in abundance and statistical significance of proteins in XPO1E571K/WT versus XPO1WT NALM-6 cells detected by SILAC analysis of cytoplasmic fractions

Altered expression of XPO1, the main nuclear export receptor in eukaryotic cells, has been observed in cancer, and XPO1 has been a focus of anticancer drug development. However, mechanistic evidence for cancer-specific alterations in XPO1 function is lacking. Here, genomic analysis of 42,793 cancers identified recurrent and previously unrecognized mutational hotspots in XPO1. XPO1 mutations exhibited striking lineage specificity, with enrichment in a variety of B-cell malignancies, and introduction of single amino acid substitutions in XPO1 initiated clonal, B-cell malignancy in vivo. Proteomic characterization identified that mutant XPO1 altered the nucleocytoplasmic distribution of hundreds of proteins in a sequence-specific manner that promoted oncogenesis. XPO1 mutations preferentially sensitized cells to inhibitors of nuclear export, providing a biomarker of response to this family of drugs. These data reveal a new class of oncogenic alteration based on change-of-function mutations in nuclear export signal recognition and identify therapeutic targets based on altered nucleocytoplasmic trafficking.Significance:Here, we identify that heterozygous mutations in the main nuclear exporter in eukaryotic cells, XPO1, are positively selected in cancer and promote the initiation of clonal B-cell malignancies. XPO1 mutations alter nuclear export signal recognition in a sequence-specific manner and sensitize cells to compounds in clinical development inhibiting XPO1 function.This article is highlighted in the In This Issue feature, p. 1325

Characteristics of XPO1 mutant and wild-type CLL patients that underwent RNA-sequencing analysis.

Supplementary Table Captions for Tables S1-S6

Proteins with predicted or known nuclear export signals and significantly enhanced or reduced in nuclear export in XPO1 mutant versus wild-type from SILAC analysis.

Supplementary Methods

Transcription and pre-mRNA splicing are key steps in the control of gene expression and mutations in genes regulating each of these processes are common in leukaemia1,2. Despite the frequent overlap of mutations affecting epigenetic regulation and splicing in leukaemia, how these processes influence one another to promote leukaemogenesis is not understood and, to our knowledge, there is no functional evidence that mutations in RNA splicing factors initiate leukaemia. Here, through analyses of transcriptomes from 982 patients with acute myeloid leukaemia, we identified frequent overlap of mutations in IDH2 and SRSF2 that together promote leukaemogenesis through coordinated effects on the epigenome and RNA splicing. Whereas mutations in either IDH2 or SRSF2 imparted distinct splicing changes, co-expression of mutant IDH2 altered the splicing effects of mutant SRSF2 and resulted in more profound splicing changes than either mutation alone. Consistent with this, co-expression of mutant IDH2 and SRSF2 resulted in lethal myelodysplasia with proliferative features in vivo and enhanced self-renewal in a manner not observed with either mutation alone. IDH2 and SRSF2 double-mutant cells exhibited aberrant splicing and reduced expression of INTS3, a member of the integrator complex3, concordant with increased stalling of RNA polymerase II (RNAPII). Aberrant INTS3 splicing contributed to leukaemogenesis in concert with mutant IDH2 and was dependent on mutant SRSF2 binding to cis elements in INTS3 mRNA and increased DNA methylation of INTS3. These data identify a pathogenic crosstalk between altered epigenetic state and splicing in a subset of leukaemias, provide functional evidence that mutations in splicing factors drive myeloid malignancy development, and identify spliceosomal changes as a mediator of IDH2-mutant leukaemogenesis. Analyses of transcriptomes from patients with acute myeloid leukaemia identified frequently co-occurring mutations of IDH2 and SRSF2, which functional analyses showed to have distinct and coordinated leukaemogenic effects on the epigenome and RNA splicing.

Mutations in genes involved in DNA methylation (DNAme; for example, TET2 and DNMT3A) are frequently observed in hematological malignancies1–3 and clonal hematopoiesis4,5. Applying single-cell sequencing to murine hematopoietic stem and progenitor cells, we observed that these mutations disrupt hematopoietic differentiation, causing opposite shifts in the frequencies of erythroid versus myelomonocytic progenitors following Tet2 or Dnmt3a loss. Notably, these shifts trace back to transcriptional priming skews in uncommitted hematopoietic stem cells. To reconcile genome-wide DNAme changes with specific erythroid versus myelomonocytic skews, we provide evidence in support of differential sensitivity of transcription factors due to biases in CpG enrichment in their binding motif. Single-cell transcriptomes with targeted genotyping showed similar skews in transcriptional priming of DNMT3A-mutated human clonal hematopoiesis bone marrow progenitors. These data show that DNAme shapes the topography of hematopoietic differentiation, and support a model in which genome-wide methylation changes are transduced to differentiation skews through biases in CpG enrichment of the transcription factor binding motif. Single-cell analysis of mouse hematopoietic stem cells shows that mutations in DNA methylation genes change the frequencies of erythroid versus myelomonocytic progenitors, owing to differential CpG enrichment in transcription factor binding motifs.

Somatic heterozygous mutations in spliceosome genes SRSF2, U2AF1, and SF3B1 commonly occur in patients with myeloid malignancies such as myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). Moreover, SRSF2 and U2AF1 mutations associate with poor survival and high risk of progression to AML, representing a unique genetic vulnerability for targeted therapy. We and others previously found that R-loops, a group of transcription intermediates containing RNA:DNA hybrids and displaced single-stranded DNA, are a source of genomic instability induced by different spliceosome mutants. We further showed that inhibition of ATR kinase activity preferentially kills spliceosome mutant cells in an R-loop-dependent manner. Inspired by ATR inhibition results, we performed a focused drug screen with inhibitors targeting additional DNA damage response pathways to identify novel therapeutic vulnerabilities generated by spliceosome mutations. We generated a murine leukemia model by overexpressing the MLL-AF9 fusion oncogene on an Srsf2 P95H/+background, a mutational combination that is found in ~10% of MLL-rearranged leukemias. Surprisingly, we found that Srsf2 P95H/+cells are more sensitive to five inhibitors targeting ADP-ribosyltransferases or PARP (olaparib, talazoparib, rucaparib, niraparib, veliparib) (Figs 1A-B). Olaparib (PARPi)-treated Srsf2 P95H/+cells exhibited increased apoptosis compared to Srsf2 +/+ cells as determined by AnnexinV (Fig 1C). PARPi sensitivity was also observed in isogenic murine MLL-AF9 U2af1 S34F/+cells compared to MLL-AF9 U2af1 +/+ cells (Fig 1D). These data highlight that both SRSF2 P95H and U2AF1 S34F mutations create a common vulnerability that is dependent on PARP activity for survival. To evaluate PARP activity in cells, we used isogenic K562 leukemia cells expressing SRSF2 P95H and U2AF1 S34F mutations from their endogenous loci and monitored PAR (poly(ADP-ribose)) chain levels, a marker of PARP activity. Both SRSF2 P95H and U2AF1 S34F cells exhibited elevated PAR levels compared to wildtype cells (Figs 1E-F). PARPi treatment significantly suppressed PAR signals in SRSF2 P95H and U2AF1 S34F cells. PARP inhibitors target both PARP1 and PARP2 enzymes, of which PARP1 plays a key role in DNA damage response. We used CRISPR-Cas9 to knockout PARP1 gene to determine the major PARP responsible for elevated PAR level in these leukemia cells. PARP1 deletion abrogated elevated PAR levels in U2AF1 S34F (Fig 1G) and SRSF2 P95H cells (data not shown). Altogether, we demonstrated that SRSF2 P95H and U2AF1 S34F cells trigger a PARP1 response critical for cell survival. To test whether increased PAR level arises from U2AF1 S34F-induced R-loops, we generated U2AF1 S34F cells that inducibly express RNaseH1, an enzyme that specifically cleaves the RNA moiety within RNA:DNA hybrids. Induction of RNaseH1 in U2AF1 S34F cells significantly reduced PAR levels, showing that U2AF1 S34F-induced PAR chains is R-loop-dependent (Fig 1H). Moreover, RNaseH1 overexpression suppressed the growth inhibition of PARPi-treated U2AF1 S34F cells (Fig 1I). Collectively, these results suggest that U2AF1 S34F mutants induce R-loop accumulation and elicit an R-loop-associated PARP1 signaling to promote cell survival. We next tested whether combining ATR inhibitor (ATRi) can further exacerbate PARPi sensitivity in spliceosome mutant cells. To examine ATR activity, we monitored phosphorylated RPA (Replication Protein A, or pRPA), a known ATR substrate. pRPA level was enhanced in PARPi-treated SRSF2 P95H cells compared to PARPi-treated SRSF2 WT cells but was suppressed when treated with ATRi (Fig 1J), suggesting that splicing factor mutant cells are more reliant on ATR function in the context of PARPi. Importantly, the combination of PARPi with ATRi, but not with ATMi, significantly promoted cell growth inhibition in SRSF2 P95H cells compared to SRSF2 WT cells or to SRSF2 P95H cells treated with individual compounds alone (Fig 1K). Collectively, these data provide a pre-clinical rationale that splicing factor mutant leukemias are preferentially sensitive to PARP1 modulation compared to their wildtype counterpart. Moreover, combining PARPi and ATRi may further sensitize spliceosome mutant cells and could represent a new therapeutic strategy in myeloid leukemia patients harboring these mutations (Fig 1L). Figure 1 Figure 1. Disclosures Graubert: Calico: Research Funding; Janssen: Research Funding; astrazeneca: Research Funding.

Chronic myelomonocytic leukemia (CMML) and juvenile myelomonocytic leukemia (JMML) are myelodysplastic syndrome (MDS)/myeloproliferative neoplasm (MPN) overlap disorders characterized by monocytosis, myelodysplasia, and a characteristic hypersensitivity to granulocyte-macrophage colony-stimulating factor (GM-CSF). Currently, there are no available disease-modifying therapies for CMML, nor are there preclinical models that fully recapitulate the unique features of CMML. Through use of immunocompromised mice with transgenic expression of human GM-CSF, interleukin-3, and stem cell factor in a NOD/SCID-IL2Rγnull background (NSGS mice), we demonstrate remarkable engraftment of CMML and JMML providing the first examples of serially transplantable and genetically accurate models of CMML. Xenotransplantation of CD34+ cells (n = 8 patients) or unfractionated bone marrow (BM) or peripheral blood mononuclear cells (n = 10) resulted in robust engraftment of CMML in BM, spleen, liver, and lung of recipients (n = 82 total mice). Engrafted cells were myeloid-restricted and matched the immunophenotype, morphology, and genetic mutations of the corresponding patient. Similar levels of engraftment were seen upon serial transplantation of human CD34+ cells in secondary NSGS recipients (2/5 patients, 6/11 mice), demonstrating the durability of CMML grafts and functionally validating CD34+ cells as harboring the disease-initiating compartment in vivo. Successful engraftments of JMML primary samples were also achieved in all NSGS recipients (n = 4 patients, n = 12 mice). Engraftment of CMML and JMML resulted in overt phenotypic abnormalities and lethality in recipients, which facilitated evaluation of the JAK2/FLT3 inhibitor pacritinib in vivo. These data reveal that NSGS mice support the development of CMML and JMML disease-initiating and mature leukemic cells in vivo, allowing creation of genetically accurate preclinical models of these disorders.

We have recently shown that XPO1 mutations are drivers of lymphomagenesis and occur across B-cell lymphomas, specifically in chronic lymphocytic leukemia (CLL), classical Hodgkin lymphoma and primary mediastinal B-cell lymphoma. The co-occurrence of other oncogenic events cooperating with XPO1 provides an opportunity for combined targeted therapy. Increased expression of the anti-apoptotic factor BCL2 has long been known to be a critical part of the pathophysiology of B-cell lymphomas. Recently, the oral BCL2 inhibitor, venetoclax, was approved in CLL and is currently being evaluated in clinical trials for other B-cell lymphomas. Selinexor is a potent, oral XPO1 inhibitor that was recently approved in multiple myeloma and diffuse large B-cell lymphoma. XPO1 inhibition exerts its antineoplastic effects by blocking key lymphomagenic pathways, such as NFκB, and decreasing the anti-apoptotic protein survivin. We therefore hypothesized that combining selinexor and venetoclax would have potential synergy and provide an oral precision combination therapy for relapsed, refractory lymphoma. We first set out to determine whether XPO1 mutant lymphoma cell lines showed differential response to either selinexor or venetoclax monotherapy. Five lymphoma cell lines; 3 diffuse large B-cell lymphoma (SU-DHL-6, SU-DHL-16, FARAGE) and 2 classical Hodgkin lymphoma (L428 and SUP-HD1), were subjected to next-generation sequencing (NGS) to assess for the presence or absence of XPO1 mutations. SUDHL-16 and SUP-HD1 were heterozygous for the XPO1 E571K hotspot mutation while SUDHL-6, FARAGE and SUP-HD1 were wildtype at the XPO1 locus. These 5 cell lines were used to assess sensitivity to Selinexor and/or Venetoclax. The CellTiter Glo assay was used to assess cell viability after 72 hours of treatment. Assays were performed in triplicate on 96-well plates that were read using a Spectramax plate reader. The XPO1 mutant cells showed increased sensitivity to selinexor (XPO1 mutant IC50 = 16-35nM; XPO1 WT IC50 = 41-231nM) as previously seen in conditional knockin mouse models of XPO1 mutant CLL (Figure A). Additionally, the XPO1 mutant cell lines showed increased sensitivity to single-agent venetoclax (XPO1 mutant IC50 = 2-13nM; XPO1 WT IC50 = 5-2853nM), an observation that has not previously been made (Figure B). Next, we tested the synergy of the combination of selinexor and venetoclax in the XPO1 mutant and wildtype cell lines. Increasing concentrations of the individual drugs were applied to each individual cell line in a 6x6 matrix. The cell viability percentage for each concentration was then entered into a synergy finder (www. synergyfinder.fimm.fi). The Bliss Independence model was used to calculate synergy of the Selinexor-Venetoclax combinations. As hypothesized, the combination of selinexor and venetoclax indeed showed synergy in both the wildtype and mutant XPO1 cell lines. Furthermore, the XPO1 mutant cell lines showed a higher degree of synergy compared to the wildtype cells (Figure C). Finally, a remarkable patient allowed us to test this combination ex vivo. This patient with CLL had undergone multiple therapies including chemoimmunotherapy, ibrutinib and venetoclax monotherapies. This patient had a founder XPO1 E571K mutation and also had acquired a BTK C481S ibrutinib resistance mutation and MYC amplification. These cells were unique in that they were easily able to be tested in ex-vivo culture to test sensitivity to different therapies. When tested with chemotherapy or ibrutinib they were completely resistant, and even with venetoclax they were fairly resistant; however, they remained sensitive to XPO1 inhibition with Selinexor. Selinexor and venetoclax showed remarkable synergy measured by a BLISS delta score of 18.78 (Figure D). In conclusion, inhibiting the nuclear exporter XPO1 and the anti-apoptotic factor BCL2 is synergistic in both XPO1 wildtype and mutant lymphoma. XPO1 mutant lymphomas show increased sensitivity to both selinexor and venetoclax. Additionally, selinexor and venetoclax showed a higher degree of synergism in XPO1 mutant lymphoma cell lines and were highly synergistic in primary XPO1 mutant CLL patient cells ex vivo. This combination is highly promising as an all oral alternative for relapsed, refractory lymphoma. Next steps include preclinical testing in mouse models in vivo using XPO1 mutant and wildtype mice crossed with mice overexpressing BCL2. Figure Disclosures No relevant conflicts of interest to declare.

Although mutations in the gene encoding the RNA splicing factor SF3B1 are frequent in multiple cancers, their functional effects and therapeutic dependencies are poorly understood. Here, we characterize 98 tumors and 12 isogenic cell lines harboring SF3B1 hotspot mutations, identifying hundreds of cryptic 3′ splice sites common and specific to different cancer types. Regulatory network analysis revealed that the most common SF3B1 mutation activates MYC via effects conserved across human and mouse cells. SF3B1 mutations promote decay of transcripts encoding the protein phosphatase 2A (PP2A) subunit PPP2R5A, increasing MYC S62 and BCL2 S70 phosphorylation which, in turn, promotes MYC protein stability and impair apoptosis, respectively. Genetic PPP2R5A restoration or pharmacologic PP2A activation impaired SF3B1-mutant tumorigenesis, elucidating a therapeutic approach to aberrant splicing by mutant SF3B1. Significance: Here, we identify that mutations in SF3B1, the most commonly mutated splicing factor gene across cancers, alter splicing of a specific subunit of the PP2A serine/threonine phosphatase complex to confer post-translational MYC and BCL2 activation, which is therapeutically intervenable using an FDA-approved drug. See related commentary by O'Connor and Narla, p. 765. This article is highlighted in the In This Issue feature, p. 747

Since the discovery of RNA splicing more than 40 years ago, our comprehension of the molecular events orchestrating constitutive and alternative splicing has greatly improved. Dysregulation of pre‐mRNA splicing has been observed in many human diseases including neurodegenerative diseases and cancer. The recent identification of frequent somatic mutations in core components of the spliceosome in myeloid malignancies and functional analysis using model systems has advanced our knowledge of how splicing alterations contribute to disease pathogenesis. In this review, we summarize our current understanding on the mechanisms of how mutant splicing factors impact splicing and the resulting functional and pathophysiological consequences. We also review recent advances to develop novel therapeutic approaches targeting splicing catalysis and splicing regulatory proteins, and discuss emerging technologies using oligonucleotide‐based therapies to modulate pathogenically spliced isoforms.

Cancer-associated mutations in genes encoding RNA splicing factors (SFs) commonly occur in leukemias, as well as in a variety of solid tumors, and confer dependence on wild-type splicing. These observations have led to clinical efforts to directly inhibit the spliceosome in patients with refractory leukemias. Here, we identify that inhibiting symmetric or asymmetric dimethylation of arginine, mediated by PRMT5 and type I protein arginine methyltransferases (PRMTs), respectively, reduces splicing fidelity and results in preferential killing of SF-mutant leukemias over wild-type counterparts. These data identify genetic subsets of cancer most likely to respond to PRMT inhibition, synergistic effects of combined PRMT5 and type I PRMT inhibition, and a mechanistic basis for the therapeutic efficacy of PRMT inhibition in cancer.

A number of recent studies have highlighted that splicing is frequently altered in cancer and that mutations affecting splicing of key cancer-associated genes as well as mutations and copy-number changes affecting spliceosomal proteins themselves are enriched in cancer. In parallel, there is also accumulating evidence that several molecular subtypes of cancer are highly dependent on wildtype splicing function for cell survival. These findings have resulted in a growing interest in targeting splicing catalysis, splicing regulatory proteins, and/or individual key altered splicing events in the treatment of cancer. In this review we present strategies that exist and are in development to target altered dependency on the spliceosome as well as aberrant splicing in cancer. These include drugs to target global splicing in cancer subtypes which are preferentially dependent on wildtype splicing for survival, methods to alter post-translational modifications of splice regulatory proteins, and strategies to modulate pathologic splicing events and protein/RNA interactions in cancer.

Mutations in genes encoding splicing factors (which we refer to as spliceosomal genes) are commonly found in patients with myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). These mutations recurrently affect specific amino acid residues, leading to perturbed normal splice site and exon recognition. Spliceosomal gene mutations are always heterozygous and rarely occur together with one another, suggesting that cells may tolerate only a partial deviation from normal splicing activity. To test this hypothesis, we engineered mice to express a mutated allele of serine/arginine-rich splicing factor 2 (Srsf2(P95H))-which commonly occurs in individuals with MDS and AML-in an inducible, hemizygous manner in hematopoietic cells. These mice rapidly succumbed to fatal bone marrow failure, demonstrating that Srsf2-mutated cells depend on the wild-type Srsf2 allele for survival. In the context of leukemia, treatment with the spliceosome inhibitor E7107 (refs. 7,8) resulted in substantial reductions in leukemic burden, specifically in isogenic mouse leukemias and patient-derived xenograft AMLs carrying spliceosomal mutations. Whereas E7107 treatment of mice resulted in widespread intron retention and cassette exon skipping in leukemic cells regardless of Srsf2 genotype, the magnitude of splicing inhibition following E7107 treatment was greater in Srsf2-mutated than in Srsf2-wild-type leukemia, consistent with the differential effect of E7107 on survival. Collectively, these data provide genetic and pharmacologic evidence that leukemias with spliceosomal gene mutations are preferentially susceptible to additional splicing perturbations in vivo as compared to leukemias without such mutations. Modulation of spliceosome function may thus provide a new therapeutic avenue in genetically defined subsets of individuals with MDS or AML.

In this issue of Blood, Nakata et al demonstrate that hematopoietic-specific expression of a mutation in the E3 ubiquitin ligase Casitas B cell lymphoma (CBL) results in a disorder that recapitulates the key features of human chronic myelomonocytic leukemia (CMML). One of the challenges currently facing researchers studying CMML is the scarcity of faithful model systems to study disease pathogenesis and therapeutic response. Given the lack of curative therapy for most patients with CMML, there is a pressing need to develop improved preclinical models to inform mechanistic studies and drug development. Although genetically engineered murine models exist for the 3 most commonly mutated genes in CMML, SRSF2, TET2, and ASXL1, none of these models recapitulates the entire phenotypic spectrum of human CMML, including chronic elevation in monocytes, multilineage dysplasia, hypersensitivity to cytokines, and susceptibility to transformation to acute myeloid leukemia (AML).

Polycomb repressive complex 2 (PRC2) is a chromatin modifier that regulates stem cells in embryonic and adult tissues. Loss-of-function studies of PRC2 components have been complicated by early embryonic dependence on PRC2 activity and the partial functional redundancy of enhancer of zeste homolog 1 (Ezh1) and enhancer of zeste homolog 2 (Ezh2), which encode the enzymatic component of PRC2. Here, we investigated the role of PRC2 in hematopoiesis by conditional deletion of suppressor of zeste 12 protein homolog (Suz12), a core component of PRC2. Complete loss of Suz12 resulted in failure of hematopoiesis, both in the embryo and the adult, with a loss of maintenance of hematopoietic stem cells (HSCs). In contrast, partial loss of PRC2 enhanced HSC self-renewal. Although Suz12 was required for lymphoid development, deletion in individual blood cell lineages revealed that it was dispensable for the development of granulocytic, monocytic, and megakaryocytic cells. Collectively, these data reveal the multifaceted role of PRC2 in hematopoiesis, with divergent dose-dependent effects in HSC and distinct roles in maturing blood cells. Because PRC2 is a potential target for cancer therapy, the significant consequences of modest changes in PRC2 activity, as well as the cell and developmental stage-specific effects, will need to be carefully considered in any therapeutic context.

Polycomb repressive complex 2 (PRC2) plays a key role in hematopoietic stem and progenitor cell (HSPC) function. Analyses of mouse mutants harboring deletions of core components have implicated PRC2 in fine-tuning multiple pathways that instruct HSPC behavior, yet how PRC2 is targeted to specific genomic loci within HSPCs remains unknown. Here we use short hairpin RNA-mediated knockdown to survey the function of PRC2 accessory factors that were defined in embryonic stem cells (ESCs) by testing the competitive reconstitution capacity of transduced murine HSPCs. We find that, similar to the phenotype observed upon depletion of core subunit Suz12, depleting Jarid2 enhances the competitive transplantation capacity of both fetal and adult mouse HSPCs. Furthermore, we demonstrate that depletion of JARID2 enhances the in vitro expansion and in vivo reconstitution capacity of human HSPCs. Gene expression profiling revealed common Suz12 and Jarid2 target genes that are enriched for the H3K27me3 mark established by PRC2. These data implicate Jarid2 as an important component of PRC2 that has a central role in coordinating HSPC function.

Additional sex combs-like (ASXL) proteins are mammalian homologues of additional sex combs (Asx), a regulator of trithorax and polycomb function in Drosophila. While there has been great interest in ASXL1 due to its frequent mutation in leukemia, little is known about its paralog ASXL2, which is frequently mutated in acute myeloid leukemia patients bearing the RUNX1-RUNX1T1 (AML1-ETO) fusion. Here we report that ASXL2 is required for normal haematopoiesis with distinct, non-overlapping effects from ASXL1 and acts as a haploinsufficient tumour suppressor. While Asxl2 was required for normal haematopoietic stem cell self-renewal, Asxl2 loss promoted AML1-ETO leukemogenesis. Moreover, ASXL2 target genes strongly overlapped with those of RUNX1 and AML1-ETO and ASXL2 loss was associated with increased chromatin accessibility at putative enhancers of key leukemogenic loci. These data reveal that Asxl2 is a critical regulator of haematopoiesis and mediates transcriptional effects that promote leukemogenesis driven by AML1-ETO., While the role of ASLX1 in haematopoiesis and leukaemia has been heavily studied, the role of ASLX2 is unclear. Here the authors show that ASLX2 is required for normal haematopoietic stem cell self-renewal whereas Asxl2 loss promotes leukemogenesis, thus explaining the frequently observed mutations in AML patients

Mutations affecting RNA splicing factors are the most common genetic alterations in myelodysplastic syndrome (MDS) patients and occur in a mutually exclusive manner. The basis for the mutual exclusivity of these mutations and how they contribute to MDS is not well understood. Here we report that although different spliceosome gene mutations impart distinct effects on splicing, they are negatively selected for when co-expressed due to aberrant splicing and downregulation of regulators of hematopoietic stem cell survival and quiescence. In addition to this synthetic lethal interaction, mutations in the splicing factors SF3B1 and SRSF2 share convergent effects on aberrant splicing of mRNAs that promote nuclear factor κB signaling. These data identify shared consequences of splicing-factor mutations and the basis for their mutual exclusivity.

Genomic analyses of cancer have identified recurrent point mutations in the RNA splicing factor–encoding genes SF3B1, U2AF1, and SRSF2 that confer an alteration of function(1–6). Cancer cells bearing these mutations are preferentially dependent on wild-type (WT) spliceosome function(7–11), but clinically relevant means to therapeutically target the spliceosome do not currently exist. Here we describe an orally available modulator of the SF3b complex, H3B-8800, which potently and preferentially kills spliceosome-mutant epithelial and hematologic tumor cells. These killing effects of H3B-8800 are due to its direct interaction with the SF3b complex, as evidenced by loss of H3B-8800 activity in drug-resistant cells bearing mutations in genes encoding SF3b components. Although H3B-8800 modulates WT and mutant spliceosome activity, the preferential killing of spliceosome-mutant cells is due to retention of short, GC-rich introns, which are enriched for genes encoding spliceosome components. These data demonstrate the therapeutic potential of splicing modulation in spliceosome-mutant cancers.

Paroxysmal nocturnal hemoglobinuria (PNH) is a nonmalignant clonal disease of hematopoietic stem cells that is associated with hemolysis, marrow failure, and thrombophilia. PNH has been considered a monogenic disease that results from somatic mutations in the gene encoding PIGA, which is required for biosynthesis of glycosylphosphatidylinisotol-anchored (GPI-anchored) proteins. The loss of certain GPI-anchored proteins is hypothesized to provide the mutant clone with an extrinsic growth advantage, but some features of PNH argue that there are intrinsic drivers of clonal expansion. Here, we performed whole-exome sequencing of paired PNH+ and PNH- fractions on samples taken from 12 patients as well as targeted deep sequencing of an additional 36 PNH patients. We identified additional somatic mutations that resulted in a complex hierarchical clonal architecture, similar to that observed in myeloid neoplasms. In addition to mutations in PIGA, mutations were found in genes known to be involved in myeloid neoplasm pathogenesis, including TET2, SUZ12, U2AF1, and JAK2. Clonal analysis indicated that these additional mutations arose either as a subclone within the PIGA-mutant population, or prior to PIGA mutation. Together, our data indicate that in addition to PIGA mutations, accessory genetic events are frequent in PNH, suggesting a stepwise clonal evolution derived from a singular stem cell clone.

Inversions between chromosome 3q21 and 3q26 ("inv(3)/t(3;3)") mark an aggressive, poor prognosis form of AML with limited treatment options and also occasionally occur in MDS and CML. Inv(3)/t(3;3) repositions a distal GATA2enhancer from 3q21 to the EVI1locus at 3q26 inducing ectopic EVI1 expression and reducing GATA2 expression. At the same time, additional genomic alterations exist in inv(3)/t(3;3) leukemias but the contributions of these events to inv(3)/t(3;3) leukemia are not well understood. Here we evaluated genomic alterations in 63 patients with inv(3)/t(3;3) leukemia. Mutations in NRAS and the core RNA splicing factor SF3B1 were the most common individual alterations (each occurring in 27% of patients; Fig.A). We next quantified gene expression and splicing in AML samples with and without inv(3)/t(3;3) abnormalities and SF3B1 mutations. Amongst inv(3)/t(3;3) AML, the majority of gene expression changes were driven by the inv(3)/t(3;3) rearrangement while the majority of splicing changes were driven by mutant SF3B1. The most abundant category of splicing change in inv(3)/SF3B1 co-mutant cells was alteration in 3' splice site usage (Fig.B). Intriguingly, one of the most robust changes in splicing in inv3/SF3B1 co-mutant cells was aberrant splicing of EVI1itself such that SF3B1 mutant cells promoted expression of a novel isoform of EVI1using an intron proximal 3' splice site (Fig.C; the official gene name "MECOM" corresponds to the genes MDS1and EVI1at this locus). While several mRNA isoforms of EVI1have been previously described, these all result in loss of EVI1 functional domains. In contrast, the unique EVI1 isoform in SF3B1 mutant/inv(3) AMLs contains in an in-frame insertion of six amino acids in the second zinc finger domain (ZF2) of EVI1 (a region of EVI1 known to be affected by germline mutations in leukemia predisposition syndromes). These data identify that nearly one-third of inv(3) AML patients express a heretofore undescribed isoform of EVI1. Of note, this unannotated EVI1isoform is also present in EVI1expressing/SF3B1K700Emutant leukemias lacking inv(3)). The above findings highlight a novel model where inv(3)/t(3;3) AML is driven by ectopic expression of distinct oncogenic isoforms of EVI1. To test this model and understand the contribution of SF3B1K700Eto inv(3)/t(3;3) AML, we crossed transgenic mice bearing the entire human inv(3)(q21;q26) locus whereby the GATA2enhancer misdirects human EVI1expression ("inv3 mice"; Yamazaki et al. Cancer Cell2014) to Sf3b1K700Econditional knockin mice (Mx1-cre Sf3b1K700E/WT).Given that the human MECOMlocus (coding and noncoding regions) was recapitulated in this mouse model, the concordant novel EVI1isoform was expressed in inv3/Sf3b1K700Emice as in patients. While Mx1-cre Sf3b1K700Emice develop an MDS-like disorder, inv3 mice develop myeloid and lymphoid leukemias with lethality ~300 days after birth. However, expression of the Sf3b1K700E/WTmutation in inv3 hematopoietic cells resulted in a highly penetrant MDS, which transformed to a lethal AML by a median of 241 days (Fig.D;p=0.0021). In the first 6 months following transplant, Mx1-cre inv3 Sf3b1K700Emice had leukopenia, macrocytic anemia, and morphologic dysplasia (Fig.E-F) that eventually transformed to a disease with a high WBC count and large numbers of immature cells around time of death. In competitive reconstitution assays, Mx1-cre inv3 Sf3b1K700Ehematopoietic stem cells (HSCs) failed to differentiate into mature peripheral blood cells despite having a competitive advantage at the level of HSCs (Fig.G-H). RNA-seq of hematopoietic precursors from the above models identified (i) a substantial change in splicing in inv3/Sf3b1K700Emutant leukemias versus those driven by inv3 alone, and (ii) alterations in a host of RNA binding proteins in inv3/Sf3b1K700Emutant leukemias (Fig.I). These data highlight a high occurrence of SF3B1 mutations in inv(3)/t(3;3) leukemias, present a new genetically accurate model for inv(3) AML, and uncover a novel oncogenic isoform of EVI1 expressed in a large proportion of inv(3)/t(3;3) patients. Ongoing work focused on identifying the mechanistic effect of the SF3B1-mutant induced aberrant EVI1isoform may provide novel insight into the role of EVI1 in promoting leukemogenesis and engender development of therapeutic opportunities targeting EVI1splicing. Figure Disclosures No relevant conflicts of interest to declare.

Mutations in the RNA splicing factor SF3B1 are common in MDS and other myeloid malignancies. SF3B1 mutations promote expression of mRNAs that use an aberrant, intron proximal 3' splice site (ss). Despite the consistency of this finding, linking aberrant splicing changes to disease pathogenesis has been a challenge. Here we identify aberrant splicing and downregulated expression of BRD9, a member of the recently described ATP-dependent non-canonical BAF (ncBAF) chromatin remodeling complex, across SF3B1 mutant leukemias. In so doing, we identify a novel role for altered ncBAF function in hematopoiesis and MDS. To systematically identify functionally important aberrant splicing events created by mutant SF3B1, we integrated differential splicing events in SF3B1 mutant versus wild-type MDS with a positive enrichment CRISPR screen mimicking splicing changes induced by mutant SF3B1 that promote NMD (non-sense mediated mRNA decay). We tested whether loss of any gene functionally inactivated by SF3B1 mutations promoted transformation of Ba/F3 and 32D cells. This identified a specific NMD-inducing aberrant splicing event in BRD9 which promoted cytokine independence (Fig. A) and exhibited striking aberrant splicing across CLL and MDS and across all mutational hotspots in SF3B1 (Fig. B). SF3B1 mutations cause exonization of a normally intronic sequence in BRD9, resulting in inclusion of a poison exon that interrupts BRD9's reading frame (Fig. C) and reduced BRD9 mRNA and protein expression through NMD (Fig. D). We confirmed that mutant SF3B1 suppressed full-length BRD9 levels without generating truncated BRD9 protein. Loss of BRD9 impaired ncBAF complex formation as indicated by abolished interaction between the ncBAF specific component GLTSCR1 and the ATPase subunit BRG1 upon chemical or spliceosomal BRD9 ablation (Fig. D). Given that prior work has linked mutant SF3B1 to use of aberrant 3' ss, we sought to understand the molecular basis for aberrant exon inclusion in BRD9 by mutant SF3B1. Lariat sequencing of SF3B1 mutant versus WT K562 cells and BRD9 minigene analyses identified use of a deep intronic branchpoint adenosine by mutant SF3B1 to promote BRD9 poison exon inclusion (Fig. E). The data above suggest a role for BRD9 downregulation in SF3B1 mutant leukemia. While prior work indicated that BRD9 is required in MLL-rearranged AML (Hohmman et al. Nature Chemical Biology 2016), the role of BRD9 in normal hematopoiesis or other subtypes of myeloid neoplasms has not been evaluated. Genetic downregulation of BRD9 in normal human hematopoietic progenitors from cord blood promoted myelopoiesis while impairing megakaryopoiesis. Interestingly and unexpectedly, BRD9 loss in CD34+ cells promoted terminal erythroid differentiation in vitro. To further evaluate BRD9's role in hematopoiesis in vivo, we also generated mice with inducible knockout of the bromodomain of BRD9 (required for BRD9 function) and generation of a frameshift transcript resulting in reduced Brd9 expression (Fig. F). Loss of Brd9 resulted in macrocytosis with bone marrow erythroid dysplasia in a dosage-dependent manner, along with impaired lymphopoiesis and myeloid skewing. Moreover, competitive transplantation of hematopoietic precursors from these mice revealed that ablation of Brd9 function impaired lymphoid reconstitution while promoting advantage of myeloid cells and hematopoietic precursors (Fig. G-I). In myeloid leukemia cells, introduction of SF3B1K700E or downregulation of BRD9 resulted in increased chromatin accessibility at promoters with a significant overlap in commonly upregulated genes. This finding suggests shared epigenetic effects of SF3B1K700E mutations and BRD9 loss (Fig. J). These data identify aberrant splicing of BRD9 across the spectrum of SF3B1 mutant cancers and identify a novel role for downregulation of ncBAF function in MDS pathogenesis. Consistent with human genetic data, genetic ablation of BRD9 function in mouse and human hematopoietic cells resulted in myeloid skewing and dyserythropoiesis. These data suggest that targeted correction of aberrant BRD9 splicing might serve as a novel therapeutic approach for SF3B1-mutant leukemias. Of note, treatment with drugs impairing the binding of mutant SF3B1 to RNA resulted in a dose-dependent rescue of aberrant BRD9 splicing in vitro (Fig. K) and in treatment of an SF3B1 mutant AML patient-derived xenograft in vivo. Figure Disclosures Kadoch: Foghorn Therapeutics: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees.

Deregulation of polycomb group complexes polycomb repressive complex 1 (PRC1) and 2 (PRC2) is associated with human cancers. Although inactivating mutations in PRC2-encoding genes EZH2, EED, and SUZ12 are present in T-cell acute lymphoblastic leukemia and in myeloid malignancies, gain-of-function mutations in EZH2 are frequently observed in B-cell lymphoma, implying disease-dependent effects of individual mutations. We show that, in contrast to PRC1, PRC2 is a tumor suppressor in Eµ-myc lymphomagenesis, because disease onset was accelerated by heterozygosity for Suz12 or by short hairpin RNA-mediated knockdown of Suz12 or Ezh2. Accelerated lymphomagenesis was associated with increased accumulation of B-lymphoid cells in the absence of effects on apoptosis or cell cycling. However, Suz12-deficient B-lymphoid progenitors exhibit enhanced serial clonogenicity. Thus, PRC2 normally restricts the self-renewal of B-lymphoid progenitors, the disruption of which contributes to lymphomagenesis. This finding provides new insight regarding the functional contribution of mutations in PRC2 in a range of leukemias.

SMCHD1 is an epigenetic modifier of gene expression that is critical to maintain X chromosome inactivation. Here, we show in mouse that genetic inactivation of Smchd1 accelerates tumorigenesis in male mice. Loss of Smchd1 in transformed mouse embryonic fibroblasts increased tumor growth upon transplantation into immunodeficient nude mice. In addition, loss of Smchd1 in Eμ-Myc transgenic mice that undergo lymphomagenesis reduced disease latency by 50% relative to control animals. In premalignant Eμ-Myc transgenic mice deficient in Smchd1, there was an increase in the number of pre-B cells in the periphery, likely accounting for the accelerated disease in these animals. Global gene expression profiling suggested that Smchd1 normally represses genes activated by MLL chimeric fusion proteins in leukemia, implying that Smchd1 loss may work through the same pathways as overexpressed MLL fusion proteins do in leukemia and lymphoma. Notably, we found that SMCHD1 is underexpressed in many types of human hematopoietic malignancy. Together, our observations collectively highlight a hitherto uncharacterized role for SMCHD1 as a candidate tumor suppressor gene in hematopoietic cancers. Cancer Res; 73(5); 1591–9. ©2012 AACR.

Mutations in spliceosomal genes are commonly found in patients with myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML)1–3. These mutations occur at highly recurrent amino acid residues and perturb normal splice site and exon recognition4–6. Spliceosomal mutations are always heterozygous and rarely co-occur with one another, suggesting that cells may only tolerate a partial deviation from normal splicing activity. To test this hypothesis, we engineered mice that express the SRSF2P95H mutation, which commonly occurs in MDS and AML, in an inducible hemizygous manner in hematopoietic cells. These mice developed lethal bone marrow failure, demonstrating that Srsf2-mutant cells depend on the wildtype Srsf2 allele for survival. In the context of leukemia, treatment with the spliceosome inhibitor E71077,8 resulted in significant reductions in leukemic burden specifically in isogenic mouse leukemias and patient-derived xenograft (PDX) AMLs carrying spliceosomal mutations. While in vivo E7107 exposure resulted in widespread intron retention and cassette exon skipping regardless of Srsf2 genotype, the magnitude of splicing inhibition following E7107 treatment was greater in Srsf2-mutant versus wildtype leukemias, consistent with its differential effect on survival in these two genotypes. Collectively, these data provide genetic and pharmacologic evidence that leukemias with spliceosomal mutations are preferentially susceptible to additional splicing perturbations in vivo compared with wildtype counterparts. Modulation of spliceosome function may provide a novel therapeutic avenue in genetically defined subsets of MDS and AML patients.

RNA-binding proteins (RBPs) regulate many aspects of transcription and translation in a cell- and tissue-specific manner and are frequently dysregulated in malignancy. We systematically evaluated RBPs preferentially required in acute myeloid leukemia (AML) over other forms of cancer or normal hematopoietic precursors using a CRISPR/Cas9 domain-based, loss-of-function screen targeting 490 classical RBPs with 2,900 sgRNAs (Fig. A). This screen was performed in cells lines representing AML, T-cell acute lymphoblastic leukemia (T-ALL), and lung adenocarcinoma (LUAD) and revealed multiple RBPs preferentially required for AML survival, but not for T-ALL or LUAD survival. We identified genes encoding 21 RBPs that were >3-fold depleted in AML cells and significantly overexpressed in AML patient samples versus normal adult CD34+ precursors (p-value < 0.05; Fig. B). Amongst RBPs required and upregulated in AML was RBM39, an RBP described to be involved in a number of cellular processes and to interact with key splicing proteins SF3B1 and U2AF2. Genetic ablation of Rbm39 in mouse MLL-AF9 leukemia cells dramatically delayed AML development and progression (Fig. C). In parallel, it has recently been described that a class of clinically-validated anti-cancer sulfonamide compounds (including indisulam and E7820) mediate RBM39 degradation as their dominant cellular mechanism of action. This occurs via novel interactions with the DCAF15 adapter protein of the CUL4/Ddb1 ubiquitin ligase complex with RBM39 as a neo-substrate. Treatment of MOLM-13 cells xenografted into mice with indisulam conferred significant anti-leukemic effects and improved overall survival (Fig. D). To explore the mechanism of RBM39 dependence in AML, we performed proteomic analyses of RBM39 interacting proteins in MOLM-13 cells as well as transcriptome-wide analysis of RBM39 RNA binding by enhanced UV cross-linking and immunoprecipitation (eCLIP) in the same cells. RBM39 physically interacted with an entire network of RBPs identified by our CRISPR screen as crucial for AML cell survival in addition to interacting with the core SF3b splicing complex. Further, anti-RBM39 eCLIP revealed RBM39 binding to exonic regions and most enriched at exon/intron borders at 5' and 3' splice sites of pre-mRNA (Fig. E), suggesting a prominent role of RBM39 in regulating splicing. Consistent with this, RNA-sequencing of AML cells following RBM39 deletion revealed significant effects of RBM39 loss on RNA splicing, most prominently causing increased cassette exon skipping (Fig. F). Recent studies suggest that myeloid leukemias with mutations in RNA splicing factors are sensitized to pharmacologic perturbation of RNA splicing. Analysis of the effects of RBM39 degrading compounds over a panel of 18 AML cells revealed that leukemia cells bearing splicing factor mutations or with high DCAF15 expression were the most sensitive to treatment (Fig. G). Genetic introduction of SF3B1, SRSF2, or U2AF1 hotspot mutations in K562 or NALM6 cells resulted in a 20-50% reduction in IC50 in response to sulfonamides. We next performed RNA sequencing of isogenic K562 cells with or without knockin of SF3B1K700E and SRSF2P95H mutations into the endogenous loci, and treated at the IC50 of E7820 or E7107, a small molecule that inhibits the SF3b core spliceosome complex. Treatment with either drug dramatically increased cassette exon skipping events and intron retention relative to DMSO control, with greater effects in splicing mutant cells. However, at equipotent doses, E7820 markedly increased mis-splicing compared with E7107. Furthermore, E7820 treatment resulted in mis-splicing of a number of RBP targets identified in our CRISPR screen as being required for AML survival, including SUPT6H, hnRNPH, and SRSF10, as well as RBM3 and U2AF2, consistent with previous observations (Fig. H). Here through systematic evaluation of RBPs across several cancers, we identify RBPs specifically required in AML. In so doing we identify a network of functionally and physically interacting RBPs upregulated in AML over normal precursors. Genetic or pharmacologic elimination one such RBP, RBM39, led to aberrant splicing of multiple members of this RBP network as well as of transcriptional regulators required for AML survival. These data suggest important clinical potential for anti-cancer sulfonamide treatment in splicing mutant myeloid leukemias. Disclosures Uehara: Eisai: Employment. Owa:Eisai: Employment.

Genetic, epigenetic and transcriptional heterogeneity cooperate to fuel cancer's ability to evolve and adapt to therapy. In chronic lymphocytic leukemia (CLL), we have shown through bulk DNA methylation (DNAme) sequencing that the growing CLL populations diversify through stochastic DNAme changes (epimutations), impacting transcriptional heterogeneity, clonal evolution and clinical outcome. To directly integrate across epigenetic, genetic and transcriptional intra-leukemic cell-to-cell variation, we developed a high-throughput multi-modality platform that jointly interrogates the methylome, transcriptome and genetic driver mutations from the same single cell (Fig. A). We applied it to >2,000 B cells from 6 healthy donors and 12 CLL samples. We found that the common clonal CLL origin resulted in an elevated but uniform epimutation rate (i.e., low cell-to-cell epimutation variability). In contrast, in index sorted B cell subsets, ranging in maturity from naïve B cells (CD27-IgM+IgD+++IgG-) to memory B cells (CD27+IgG+), variable epimutation rates reflect cells with diverse evolutionary ages across the B cell differentiation trajectory (Fig. B). Thus, we posited that epimutation can serve as a "molecular clock", enabling high-resolution lineage reconstruction, applicable directly to patient samples. CLL lineage tree topology revealed earlier branching, and longer branch lengths than normal B cells, consistent with rapid drift after transformation, and a greater proliferative history (Fig. C). In contrast to CLL topologies, non-clonal normal B cell trees provided a smaller increase in clustering accuracy compared with parsimony-based trees (P < 0.001; Fig. D). To validate the inferred tree topology, we leveraged our multi-modal capture of DNAme and genetic drivers in single cells. Indeed, genetic subclones mapped accurately to distinct clades inferred solely based on epimutation information [e.g., a clade composed of SF3B1 mutants and another clade composed of SF3B1 wild-type cells (P = 7 x 10-9; Fig. E, F)]. Using the joint single-cell transcriptional profiling, we found that cells in SF3B1 mutated clade also displayed higher alternative 3' splicing than their wild-type counterparts (P = 0.01526; Fig. G). Cells belonging to SF3B1 mutated clade were marked by expression changes in genes related to DNA damage (e.g., KLF8) and Notch signaling (e.g., DTX4) (P < 0.05; Fig. H, I). The direct linking of single-cell transcriptional data with lineage identity also showed that transcriptional similarity between cells decreases as a function of their lineage distance (P < 0.05; Fig. K). Notably, the molecular clock feature of epimutations enabled precise timing of subclonal divergence event in the CLL's evolutionary history, estimated to have occurred 2180±219 days after the emergence of the parental clone (Fig. J). To examine potential lineage biases during therapy, we performed serial multimodal single-cell profiling of a CLL patient without subclonal genetic drivers, prior to and during ibrutinib-associated lymphocytosis. The lineage trees revealed a distinct clade of cells preferentially expelled from the lymph node, marked by a distinct transcriptional profile, likely representing ibrutinib-sensitive cells. Lastly, we hypothesized that frequent epigenetic modifier mutations seen in hematological malignancies may increase the epimutation rate promoting intra-leukemic cellular diversity. To test this hypothesis, we applied our multi-modality single-cell platform to cells from TET2 knock-out (KO) mouse models, and observed higher epimutation rates, closely associated with higher cell-to-cell transcriptional heterogeneity compared with wild-type cells (P < 0.0001; Fig. L, M). In summary, we revealed that CLL show uniformly elevated epimutation rates, reflecting the common evolutionary age of these cells. By leveraging the heritable information captured through epimutation data, we provided a native lineage tracing applicable directly to patient samples. With this approach, we showed that CLL lineage topology exhibit early branching and long-branch length, consistent with exponential growth. Finally, we demonstrated that multimodal single-cell profiling enables projection of genetic and transcriptional identity onto the lineage tree, providing a direct measurement of the heritability of transcriptional profiles as a function of lineage distance. Figure. Figure. Disclosures Wu: Neon Therapeutics: Equity Ownership.

Mutations in genes encoding RNA splicing factors constitute the most common class of genetic alterations in patients with myelodysplastic syndromes (MDS). These occur as heterozygous point mutations at specific amino acid residues in SF3B1, SRSF2, and U2AF1, and are almost always mutually exclusive with one another. Recent studies have identified that mutations in each of these genes results in activation of the innate immune signaling through altered splicing of mRNAs encoding key enzymes in this pathway. Now, through an unbiased genetic screen as well as focused genetic studies, we have identified that SF3B1-mutant MDS depends on aberrant immune signaling for cell survival. Recent work has identified that aberrant splicing of MAP3K7 (also known as TAK1; TGF-b Activating Kinase 1) is pervasive across SF3B1-mutant human and mouse cells and results in reduced MAP3K7 protein expression and increased NF-κB signaling. Consistent with this, Map3k7 haploinsufficiency in myeloid cells is known to cause myeloproliferation, while at the same time, complete loss of Map3k7 is intolerable for hematopoietic cells. We therefore hypothesized that partial inhibition of MAP3K7 might preferentially impact SF3B1-mutant cells. To test this hypothesis, we generated mice with inducible deletion of 1 or 2 copies of Map3k7 (Mx1-cre Map3k7fl/+,Mx1-cre Map3k7fl/fl) alone or in the presence of mutant Sf3b1K700E (Mx1-cre Map3k7fl/+Sf3b1K700E/+,Mx1-cre Map3k7fl/flSf3b1K700E/+), along with all controls (Mx1-cre Sf3b1+/+ Map3k7+/+ (Wildtype; WT) and Mx1-cre Sf3b1K700E/+ mice). We then performed bone marrow transplantation (BMT) to assess the effect of Map3k7 deletion on aberrant hematopoiesis driven by mutant SF3B1. Consistent with prior reports, heterozygous deletion of Map3k7did not affect repopulating potential in BMT assays compared to controls while homozygous deletion of Map3k7 resulted in complete failure of hematopoiesis (Figure A). Interestingly, however, in the presence of Sf3b1K700E mutation, deletion of a single copy of Map3k7 completely rescued the hematopoietic defects characteristic of mutant SF3B1 in both mature and immature cells (Figure B-C). These data suggest that inhibition of residual MAP3K7 function may preferentially target SF3B1-mutant MDS cells. In parallel to the above studies, we also performed a negative selection RNAi screen to uncover novel genetic dependencies in SF3B1-mutant myeloid neoplasms. We performed pooled lentiviral infection of shRNAs targeting ~2,200 genes encoding proteins which are drug targets ("The Druggable Genome") under the control of a doxycycline-inducible vector in isogenic K562 cells expressing the two most commonly occurring SF3B1 mutations, SF3B1K666N and SF3B1K700E, from the endogenous SF3B1 locus. Two individual clones per SF3B1-mutant line were used to improve the robustness of the screen. On Day 21 following shRNA activation, genes with ≥3 shRNAs depleted in SF3B1-mutant cells while remaining unchanged in parental K562 cells were selected. This identified 101 candidates that are potentially synthetic-lethal with SF3B1 mutation (Figure D). Interestingly, pathway analysis of these potential candidates revealed of genes involved in immune and inflammatory signaling as well as in metabolic processes (Figure E). Further target validation was performed using in vitro competitive growth assay in K562 cells, and another set of SF3B1 isogenic lymphoid leukemia cell lines (NALM-6) expressing the same mutations. This revealed consistent dependency of SF3B1-mutant cells on STAT1, an essential component of the interferon (IFN) signaling pathway (Figure F). Upon exposure to Type-I IFNs, SF3B1-mutant K562 cells showed increased transcriptional response in IFN-responsive genes containing interferon stimulated response elements (ISREs) compared with SF3B1 WT cells (Figure G). These data highlight that SF3B1-mutant cells are hyper-responsive to IFN signaling and require intact IFN-signaling responses for cell survival. Taken together, the above studies indicate that sustained IFN signaling as well as activated innate immune signaling downstream of TAK1 are required for the survival of SF3B1-mutant myeloid cells. These results therefore have important therapeutic implications as they suggest that pharmacologic inhibition of STAT1/Type I IFN activation and/or TAK1 may serve as important therapeutic agents for SF3B1-mutant MDS. Figure. Figure. Disclosures No relevant conflicts of interest to declare.

Mutations in the RNA splicing factor SF3B1 are recurrent in CLL and myeloid neoplasms but their functional role in promoting tumorigenesis remain poorly understood. While SF3B1 mutations have been identified as promoting use of aberrant 3' splice sites (3'ss), consistent identification of mis-spliced transcripts and pathways that functionally link mutant SF3B1 to transformation remains elusive. Moreover, large-scale analyses of the impact of mutant SF3B1 on gene expression and gene regulatory networks, which may be distinct from aberrant splicing changes, remain to be performed. We therefore sought to elucidate the effects of SF3B1 mutations across hematopoietic malignancies and cancer lineages at the level of both mRNA splicing and expression. To this end, we collected RNA-seq data from 79 tumors and 12 isogenic cell lines harboring SF3B1 hotspot mutations. The most frequent hotspot, K700E, was the most common mutation in CLL and breast cancers while mutations at position R625 were restricted to melanomas (Figure A, B). Regulatory network analysis of differentially expressed genes in SF3B1 mutated CLL identified MYC as the top master regulator (Figure C). MYC activation in SF3B1 mutated CLL was also verified by differential expression analyses (Figure D) and was common to SF3B1K700E mutant cancers while absent in cancers with mutations affecting R625. Taken together, these observations suggested that tumors harboring SF3B1K700E mutations activate the MYC transcriptional program. We next sought to verify the effects of c-Myc activation by mutant Sf3b1 in the B-cell lineage in vivo. We crossed Cd19-cre Sf3b1K700E/+ mice with Eμ-Myc transgenic mice to generate Cd19-cre+ control, Sf3b1K700E/+, Eμ-MycTg/+, and Sf3b1K700E/+Eμ-MycTg/+ double-mutant mice. While control or single mutant primary mice did not develop disease over one year, double-mutant mice developed a lethal B-cell malignancy. This effect was consistent in serial transplantation, where mice transplanted with double-mutant cells had shorter survival compared to single-mutant controls (Figure E). These data provide the first evidence that SF3B1 mutations contribute to tumorigenesis in vivo. To understand the molecular mechanism for MYC activation across SF3B1 mutant human and mouse cells, we analyzed RNA-seq data from CLL patients, isogenic Nalm-6 cells, and splenic B-cells from the mouse models. This revealed a significant overlap in aberrant (3'ss) events across SF3B1 mutant samples. Interestingly, mis-spliced events across mouse and human SF3B1K700E mutant samples identified aberrant 3'ss usage and decay of PPP2R5A (Figure F), a gene whose product has previously been shown to regulate c-MYC protein stability and the only gene whose aberrant splicing was most prominent in K700E compared with R625 mutant SF3B1. PPP2R5A is a subunit of the PP2A phosphatase complex that dephosphorylates Serine 62 (S62) of c-MYC, resulting in an unstable form of c-MYC that is a substrate for proteasomal degradation. Consistent with this, SF3B1K700E mutant cells exhibited dramatic increase in S62-phosphorylated c-MYC and increased stability of c-MYC protein. MYC expression, stability, and S62 phosphorylation could be abrogated in SF3B1 mutant cells by restoring PPP25RA expression. In addition to c-MYC S62 phosphorylation, PPP2R5A-containing PP2A reduced S70 phosphorylation of BCL2 (a modification important for apoptosis induction) in SF3B1 mutant cells. To functionally evaluate the importance of impaired PP2A enzymatic activity in SF3B1 mutant cells further, we assessed the therapeutic potential of the FDA-approved oral PP2A activator, FTY-720. SF3B1 mutant cells were more sensitive to FTY-720 treatment than SF3B1 WT counterparts, experiencing growth arrest at lower concentration (Figure G). Moreover, both S62-phosphorylated c-MYC and S70-phosphorylated BCL2 decreased in a dose-dependent manner upon treatment with FTY-720 (Figure H). Here through combined evaluation of the effects of the SF3B1 mutation on splicing, gene expression, and transcriptional networks across cancer types, we identify a novel mechanism by which mutant SF3B1-mediated alterations in RNA splicing contribute to activation of oncogenic MYC through effects on MYC proteolysis. Moreover, these data highlight a novel therapeutic approach targeting the impact of mutant SF3B1 on post-translational modification of MYC. Figure. Figure. Disclosures Mato: Janssen: Consultancy, Honoraria; Celgene: Consultancy; Prime Oncology: Speakers Bureau; TG Therapeutics: Research Funding; Regeneron: Research Funding; Abbvie: Consultancy; Sunesis: Honoraria, Research Funding; Acerta: Research Funding; AstraZeneca: Consultancy; Pharmacyclics: Consultancy, Honoraria, Research Funding.

Genomic analyses across cancer have identified recurrent somatic mutations in XPO1, which encodes a major nuclear cytoplasmic transport protein responsible for exporting a broad range of cargo proteins from the nucleus to the cytoplasm. Specifically, heterozygous mutations at the XPO1 hotspot residue E571 (most frequently E571K) are recurrent in B-cell malignancies including chronic lymphocytic leukemia, primary mediastinal B-cell lymphoma, and Hodgkin lymphoma. Despite the fact that XPO1 is the target of numerous small molecules in clinical development, functional evidence for precisely how altered XPO1 expression or mutations might promote transformation is not well delineated. We utilized genome editing to generate isogenic B-cell leukemia cells for physiologic expression of the XPO1 E571K mutation from the endogenous XPO1 locus. The heterozygous XPO1 E571K mutant cells had increased cell proliferation in vitro and in vivo relative to XPO1 wild-type (WT) counterparts. The effects of XPO1 mutation were distinct from XPO1 genetic depletion, which completely suppressed cell growth (Figure A). Given the high conservation of XPO1 across mammals, we next generated a conditional knock-in mouse model to express the Xpo1 E571K mutation from the endogenous Xpo1 locus. Cd19- Cre Xpo1 E571K/WTmice were born at normal Mendelian ratios, but were smaller than littermate controls and had increased number of B-cells in the blood and transitional (T1, T2) B-cells in the spleen with splenomegaly (Figure B). Colony forming assays in IL-7-containing methylcellulose using bone marrow (BM) from these mice revealed increased number of B-cell progenitors with enhanced clonogenicity. Given several recent reports suggesting that XPO1 mutations are clonal early events in lymphomagenesis, we also evaluated the effects of pan-hematopoietic expression of Xpo1 E571K. Transplantation of CAG- CreERT Xpo1 E571K/WTBM cells followed by tamoxifen administration to recipients resulted in skewing to B-lymphopoiesis and thrombocytopenia 12 weeks after tamoxifen induction. BM cells from CAG- CreERT Xpo1 E571K/WTshowed strikingly increased B-cell colony formation and serially replating capacity in IL-7 with reduced clonogenicity in myeloid cytokine-containing methylcellulose (Figure C). We next crossed the Cd19- Cre Xpo1 E571K/WTmice to transgenic mice with pan-hematopoietic BCL2 overexpression (vav-BCL2 mice). By 8 weeks, Cd19- Cre Xpo1 E571K/WT/ vav- BCL2 mice had higher B-cell lymphocytosis, increased B-cells in the BM and splenomegaly compared to Cd19- Cre Xpo1 WT/WT, Cd19- Cre Xpo1 E571K/WTor Cd19- Cre / vav - BCL2mice, suggesting cooperativity between the proliferative effects of XPO1 E571K and anti-apoptotic effects of BCL2 in B-cells. Moreover, B-cell progenitors from Cd19- Cre Xpo1 E571K/WT/ vav-BCL2 mice again demonstrated remarkable clonogenic capacity in IL-7-containing media compared with other genotypes. To understand the mechanism by which the XPO1 hotspot mutation confers growth-promoting effects, we performed mass spectrometry on fractionated nuclear and cytoplasmic lysates from XPO1 E571K knock-in and parental cell lines (Figure D). Numerous members of the K63-ubiquitination, TLR4, and NFκB pathways were differentially exported in XPO1 E571K mutant cells. Given the known oncogenic role of NFκB signaling in lymphoid malignancies, we further functionally evaluated this pathway. XPO1 mutant cells demonstrated differential localization of cIAP1/2, NFkBIB, IKKB, TAB2 and TRAF2. Differential export of NFκB signaling intermediates was confirmed by western blot and immunofluorescence revealing increased (but not complete) retention of cIAP1/2 proteins in the nucleus and increased levels of TRAF2 in the cytoplasm of mutant cells compared to WT. Phenotypically, XPO1 E571K cells demonstrated higher baseline NFkB signaling and transcriptional responses to stimulation with TNF-α than XPO1 WT counterpart cells (Figure E). Overall, these data identify that hotspot mutations in XPO1 promote lymphoid biased hematopoiesis and transformation by altering nuclear export of key proteins involved in hematopoietic regulation. Although numerous cellular pathways are altered in XPO1 E571K mutant cells, this mutation prominently affects compartmentalization of NFκB signaling components in a manner that promotes activation of this pathway and contributes to lymphomagenesis. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.

Histiocytic neoplasms are clonal, hematopoietic disorders characterized by an accumulation of abnormal, monocyte-derived dendritic cells or macrophages in Langerhans cell histiocytosis (LCH) and non-Langerhans cell histiocytosis (non-LCH), respectively. The discovery of BRAFV600E mutations in approximately 50% of these patients provided the first molecular therapeutic target in histiocytosis. However, recurrent driving mutations in the majority of patients with BRAFV600E–wild-type non-LCH are unknown, and recurrent cooperating mutations in non-MAP kinase pathways are undefined for the histiocytic neoplasms. Through combined whole-exome and transcriptome sequencing, we identified recurrent kinase fusions involving BRAF, ALK, and NTRK1, as well as recurrent, activating MAP2K1 and ARAF mutations in patients with BRAFV600E–wild-type non-LCH. In addition to MAP kinase pathway lesions, recurrently altered genes involving diverse cellular pathways were identified. Treatment of patients with MAP2K1- and ARAF-mutated non-LCH using MEK and RAF inhibitors, respectively, resulted in clinical efficacy, demonstrating the importance of detecting and targeting diverse kinase alterations in these disorders. Significance: We provide the first description of kinase fusions in systemic histiocytic neoplasms and activating ARAF and MAP2K1 mutations in non-Langerhans histiocytic neoplasms. Refractory patients with MAP2K1- and ARAF-mutant histiocytoses had clinical responses to MEK inhibition and sorafenib, respectively, highlighting the importance of comprehensive genomic analysis of these disorders. Cancer Discov; 6(2); 154–65. ©2015 AACR. This article is highlighted in the In This Issue feature, p. 109

Bromodomain and extra terminal protein (BET) inhibitors are first-in-class targeted therapies that deliver a new therapeutic opportunity by directly targeting bromodomain proteins that bind acetylated chromatin marks1,2. Early clinical trials have shown promise, especially in acute myeloid leukaemia3, and therefore the evaluation of resistance mechanisms is crucial to optimize the clinical efficacy of these drugs. Here we use primary mouse haematopoietic stem and progenitor cells immortalized with the fusion protein MLL-AF9 to generate several single-cell clones that demonstrate resistance, in vitro and in vivo, to the prototypical BET inhibitor, I-BET. Resistance to I-BET confers cross-resistance to chemically distinct BET inhibitors such as JQ1, as well as resistance to genetic knockdown of BET proteins. Resistance is not mediated through increased drug efflux or metabolism, but is shown to emerge from leukaemia stem cells both ex vivo and in vivo. Chromatin-bound BRD4 is globally reduced in resistant cells, whereas the expression of key target genes such as Myc remains unaltered, highlighting the existence of alternative mechanisms to regulate transcription. We demonstrate that resistance to BET inhibitors, in human and mouse leukaemia cells, is in part a consequence of increased Wnt/β-catenin signalling, and negative regulation of this pathway results in restoration of sensitivity to I-BET in vitro and in vivo. Together, these findings provide new insights into the biology of acute myeloid leukaemia, highlight potential therapeutic limitations of BET inhibitors, and identify strategies that may enhance the clinical utility of these unique targeted therapies.

During a period of acute ischemia in vivo or oxygen-glucose deprivation (OGD) in vitro, CA1 neurons depolarize, swell and become overloaded with calcium. Our aim was to test the hypothesis that the initial responses to OGD are at least partly due to transient receptor potential (TRP) channel activation. As some TRP channels are temperature-sensitive, we also compared the effects of pharmacological blockade of the channels with the effects of reducing temperature. Acute hippocampal slices (350 mum) obtained from Wistar rats were submerged in ACSF at 36 degrees C. CA1 neurons were monitored electrophysiologically using extracellular, intracellular or whole-cell patch-clamp recordings. Cell swelling was assessed by recording changes in relative tissue resistance, and changes in intracellular calcium were measured after loading neurons with fura-2 dextran. Blockers of TRP channels (ruthenium red, La3+, Gd3+, 2-APB) or lowering temperature by 3 degrees C reduced responses to OGD. This included: (a) an increased delay to negative shifts of extracellular DC potential; (b) reduction in rate of the initial slow membrane depolarization, slower development of OGD-induced increase in cell input resistance and slower development of whole-cell inward current; (c) reduced tissue swelling; and (d) a smaller rise in intracellular calcium. Mild hypothermia (33 degrees C) and La3+ or Gd3+ (100 microM) showed an occlusion effect when delay to extracellular DC shifts was measured. Expression of TRPM2/TRPM7 (oxidative stress-sensitive) and TRPV3/TRPV4 (temperature-sensitive) channels was demonstrated in the CA1 subfield with RT-PCR. These results indicate that TRP or TRP-like channels are activated by cellular stress and contribute to ischemia-induced membrane depolarization, intracellular calcium accumulation and cell swelling. We also hypothesize that closing of some TRP channels (TRPV3 and/or TRPV4) by lowering temperature may be partly responsible for the neuroprotective effect of hypothermia.

Genomic characterization of hematologic and solid cancers has revealed recurrent somatic mutations affecting genes encoding the RNA splicing factors SF3B1, U2AF1, SRSF2 and ZRSR2. Recent data reveal that these mutations confer an alteration of function inducing aberrant splicing and rendering spliceosome mutant cells preferentially sensitive to splicing modulation compared with wildtype (WT) cells. Here we describe a novel orally bioavailable small molecule SF3B1 modulator identified through a medicinal chemistry effort aimed at optimizing compounds for preferential lethality in spliceosome mutant cells. H3B-8800 potently binds to WT or mutant SF3b complexes and modulates splicing in in vitro biochemical splicing assays and cellular pharmacodynamic assays. The selectivity of H3B-8800 was confirmed by observing lack of activity in cells expressing SF3B1R1074H, the SF3B1 mutation previously shown to confer resistance to other splicing modulators. Although H3B-8800 binds both WT and mutant SF3B1, it results in preferential lethality of cancer cells expressing SF3B1K700E, SRSF2P95H, or U2AF1S34F mutations compared to WT cells. In animals xenografted with SF3B1K700E knock-in leukemia K562 cells or mice transplanted with Srsf2P95H/MLL-AF9 mouse AML cells, oral H3B-8800 treatment demonstrated splicing modulation and inhibited tumor growth, while no therapeutic impact was seen in WT controls. These data were also evident in patient-derived xenografts (PDX) from patients with CMML where H3B-8800 resulted in a substantial reduction of leukemic burden only in SRSF2-mutant but not in WT CMML PDX models. Additionally, due to the high frequency of U2AF1 mutations in non-small cell lung cancer, H3B-8800 was tested in U2AF1S34F-mutant H441 lung cancer cells. Similar to the results from leukemia models, H3B-8800 demonstrated preferential lethality of U2AF1-mutant cells in vitro and in in vivo orthotopic xenografts at well tolerated doses. RNA-seq of isogenic K562 cells treated with H3B-8800 revealed dose-dependent inhibition of splicing. Although global inhibition of RNA splicing was not observed; H3B-8800 treatment led to preferential intron retention of transcripts with shorter and more GC-rich regions compared to those unaffected by drug. Interestingly, H3B-8800-retained introns commonly disrupted the expression of spliceosomal genes, suggesting that the preferential effect of H3B-8800 on spliceosome mutant cells is due to the dependency of these cells on expression of WT spliceosomal genes. These data identify a novel therapeutic approach with selective lethality in leukemias and lung cancers bearing a spliceosome mutation. Despite the essential nature of splicing, cancer cells without a spliceosome mutation were less sensitive to H3B-8800 compared with potent eradication of mutant counterparts. H3B-8800 is currently undergoing clinical evaluation in patients with MDS, AML, and CMML. Citation Format: Silvia Buonamici, Akihide Yoshimi, Michael Thomas, Michael Seiler, Betty Chan, Benjamin Caleb, Fred Csibi, Rachel Darman, Peter Fekkes, Craig Karr, Gregg Keaney, Amy Kim, Virginia Klimek, Pavan Kumar, Kaiko Kunii, Stanley Chun-Wei Lee, Xiang Liu, Crystal MacKenzie, Carol Meeske, Yoshiharu Mizui, Eric Padron, Eunice Park, Ermira Pazolli, Sudeep Prajapati, Nathalie Rioux, Justin Taylor, John Wang, Markus Warmuth, Huilan Yao, Lihua Yu, Ping Zhu, Omar Abdel-Wahab, Peter Smith. H3B-8800, a novel orally available SF3b modulator, shows preclinical efficacy across spliceosome mutant cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1185. doi:10.1158/1538-7445.AM2017-1185

Mutations in RNA splicing factors confer an alteration of function and are common in patients with myelodysplastic syndrome (MDS, ~45%), chronic myelomonocytic leukemia (CMML, ~60%), and acute myeloid leukemia (AML) derived from these conditions. Recent data suggest that spliceosome-mutant cells are preferentially sensitive to genetic or pharmacologic splicing modulation compared with wildtype (WT) counterparts. Here, we describe the discovery of H3B-8800, a potent and orally bioavailable modulator of the SF3b complex, and demonstrate efficacy in models of spliceosome mutant myeloid malignancies including a novel xenograft system for CMML. H3B-8800 was identified through a medicinal chemistry approach aimed at identifying compounds with preferential lethality in spliceosome mutant cells. Using a scintillation proximity assay, we demonstrated that H3B-8800 potently binds to SF3b complexes containing either WT or mutant SF3B1 protein. Consistent with this, H3B-8800 showed dose-dependent modulation of splicing in in vitro biochemical splicing assays and cellular pharmacodynamic assays. Selectivity of H3B-8800 for the SF3b complex was confirmed through observing resistance in cells expressing SF3B1R1074H, an SF3B1 mutation previously shown to confer resistance to natural product splicing modulators. In the above biochemical and cellular assays, H3B-8800 affected splicing similarly regardless of spliceosome genotype. However, preferential inhibition of in vitro cell growth was observed in isogenic AML cells with endogenous knock-in of SF3B1K700E or SRSF2P95H mutations compared to WT counterparts. In animals xenografted with SF3B1K700E knock-in K562 cells, oral H3B-8800 treatment demonstrated dose-dependent splicing modulation and inhibited tumor growth, while no therapeutic impact was seen in WT controls. Similarly, anti-leukemic efficacy and improved survival were observed with H3B-8800 treatment in mice transplanted with Srsf2P95H/MLL-AF9 mouse AML cells, a result not seen in Srsf2 WT/MLL-AF9 counterpart leukemias. To understand the preferential effects on spliceosome mutant cells, RNA-seq analysis of isogenic K562 cells treated with H3B-8800 was performed. H3B-8800 induced intron retention and exon skipping, however these effects were not global and introns preferentially retained by H3B-8800 were shorter and more GC-rich compared to those unaffected by drug (Figure A). Interestingly, a substantial number of genes experiencing intron retention with H3B-8800 themselves encoded spliceosome components (Figure B). This suggests that the preferential effect of H3B-8800 on spliceosome mutant cells is due to the exquisite dependency of these cells on normal expression of spliceosome proteins. Next we aimed to understand the therapeutic potential of H3B-8800 in the context of CMML due to the high frequency of SRSF2 mutations and the need for improved outcome in this disorder. To this end, we developed a xenotransplantation model through direct intrafemoral injection of CD34+ cells from CMML patients into "NSGS" mice: a variant of NSG mice that express human IL3, SCF and GM-CSF. We specifically focused on CMML with 200,000 CD34+ cells achieved robust engraftment for all patients (n=7) with rapid lethality (median of 39 days). In vivo H3B-8800 administration substantially reduced leukemic burden in spliceosome-mutant but not spliceosome-WT CMML PDX (Figure C). Furthermore, 2.2-fold reductions in immunophenotypically-defined leukemia initiating cells were seen with H3B-8800 versus vehicle treatment in spliceosome-mutant CMML compared with no change in those mice engrafted with spliceosome-WT CMML. These data identify a novel therapeutic approach with selective lethality in myeloid cells bearing a spliceosome mutation. Despite the essential nature of splicing, CMML/AML cells without a spliceosome mutation were less sensitive to H3B-8800 compared with potent eradication of mutant counterparts. These data demonstrate the therapeutic potential of splicing modulation in spliceosome mutant cancers and H3B-8800 is currently undergoing clinical evaluation in patients with MDS, AML and CMML. Figure. Figure. Disclosures Buonamici: H3 Biomedicine: Employment. Thomas:H3 Biomedicine: Employment. Seiler:H3 Biomedicine: Employment. Chan:H3 Biomedicine: Employment. Caleb:H3 Biomedicine: Employment. Darman:H3 Biomedicine: Employment. Fekkes:H3 Biomedicine: Employment. Karr:H3 Biomedicine: Employment. Liu:H3 Biomedicine: Employment. Meeske:H3 Biomedicine: Employment. Mizui:Eisai: Employment. Pazolli:H3 Biomedicine: Employment. Prajapati:H3 Biomedicine: Employment. Wang:Eisai: Employment. Warmuth:H3 Biomedicine: Employment. Yu:H3 Biomedicine: Employment. Zhu:H3 Biomedicine: Employment. Smith:H3 Biomedicine: Employment.

Replicative immortality depends on telomerase activation in the majority of cancers including acute myeloid leukemia (AML). Imetelstat is a covalently lipidated 13-mer oligonucleotide that competitively inhibits telomerase activity. Clinical efficacy of imetelstat has recently been reported in essential thrombocythemia and myelofibrosis. We investigated the efficacy of imetelstat in AML using a randomized trial in patient-derived xenografts (PDX). To establish an AML PDX cohort, primary bone marrow (BM) or peripheral blood (PB) samples from 31 AML patients were transplanted into NOD.Cg Prkdcscid Il2rgtm1Wjl Tg (CMV-IL3,CSF2,KITLG)1Eav/Mlo (NSGS). Engraftment was defined by reconstitution of BM and spleen with CD33+ donor cells, PB circulating blasts, anemia or thrombocytopenia. The success rate for engraftment was 70.4% and was independent of cytogenetics. Fifteen independent AML patient samples (n=12 recipients/sample) were tested for efficacy of imetelstat. After engraftment, mice were randomized and treated with imetelstat (15 mg/kg body weight) or control phosphate-buffered saline (PBS) intraperitoneally every 48-72h. Across the entire cohort, survival was improved for imetelstat- vs. PBS-treated PDX (Hazard ratio PBS: 5.299; 3.379 ± 8.312; p < 0.0001; Cox proportional hazards model). Imetelstat delayed the expansion of human AML cells in 14 PDX (93.3%). AML patient samples were divided into 2 groups based on survival outcomes, "Sustained responders" (imetelstat extended survival > 2-fold or > 4 weeks; 9 AML patient samples; 60%) or "Poor responders" (6 AML patient samples, 40%). European LeukemiaNet (ELN)-karyotypic subtypes differed trend-wise between groups: favourable (100% sustained, 0% poor response to imetelstat); intermediate-1, intermediate-2 and poor (45.5% sustained, 54.5% poor response to imetelstat; p = 0.1, Fisher's exact test). Next generation sequencing revealed baseline AML PDX genetic profiles. FLT3, NRAS, TET2, RAD21 as well as 15 genes annotated in DNA damage, cell cycle regulation and apoptosis were mutated exclusively in the sustained responders group. Poor responders revealed mutations in ETV6, FANCM, MKI67, WT1 and 16 additional genes regulating growth factor independence and evasion of apoptosis. Imetelstat response was associated with reduced quiescence and induction of γ-H2AX levels in AML populations (n=4-6 / group / 3 individual AML patient samples): γ-H2AX (MFI normalized to PBS; PBS: 1.0 ± 0.02; imetelstat: 1.24 ± 0.02; p < 0.0001, Student's t test), quiescence (%Ki67-diploid AML cells; PBS: 11.62% ± 0.87; imetelstat: 6.9% ± 0.68; p < 0.001, Student's t test). The presence of spliceosome mutations (SRSF2, U2AF1) was not correlated with response (p = 0.5; Fisher's exact test). To investigate the effects on normal human hematopoiesis, CD34-enriched cord blood was transplanted into NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG, n=5-6/group/donor in 2 replicate experiments). Engraftment was confirmed at 4 weeks post-transplant by PB chimerism (>=1%). Mice were treated with imetelstat or vehicle control from 4 weeks. After 10 weeks treatment, BM cellularity and donor engraftment were significantly reduced whereas the frequency of the CD34+CD38low HSC-enriched population was unchanged (donor 1 PBS: 0.35% ± 0.03%, imetelstat: 0.23% ± 0.06%, p = 0.1; donor 2 PBS: 0.45% ± 0.05%, imetelstat: 0.92% ± 0.35%, p = 0.2, Student's t test). HSC cell cycle and γ-H2AX levels were unchanged. PB and spleen B-cell engraftment were reduced (donor 1 spleen PBS: 77.74% ± 4.66%, imetelstat: 45.48% ± 9.03%, p < 0.05; donor 2 spleen PBS: 93.95% ± 0.40%, imetelstat: 89.1% ± 2.52%, p = 0.09, Student's t test), whereas the myeloid lineage was elevated or relatively preserved (donor 1 spleen PBS: 3.29% ± 0.71%, imetelstat: 7.53% ± 1.6%, p < 0.05; donor 2 spleen PBS: 1.20% ± 0.12%, imetelstat: 4.49% ± 1.60%, p = 0.07, Student's t test). In summary, imetelstat demonstrates efficacy in a significant proportion of AML PDX (60%, 9 out of 15 individual AML patient samples). Robust responses to imetelstat were associated with favourable cytogenetic risk groups and mutations in pathways controlling DNA damage. The effects on normal human hematopoiesis were modest and predominantly seen in the B-lymphocyte lineage with relative preservation of myeloid and stem cell populations. Further study is warranted to understand the preclinical and clinical efficacy of imetelstat in AML. Disclosures Lane: Janssen: Other: i have done consulting (once) for janssen..

Mutations in genes encoding RNA splicing factors constitute the most common class of alterations in patients with myelodysplasticsyndromes (MDS). These occur predominantly as heterozygous point mutations at restricted residues in SF3B1, SRSF2, and U2AF1 in a mutually exclusive manner, suggesting that spliceosomal gene mutations confer gain-of-function with converging biological effects. However, recent studies suggest that mutations in each splicing factor result in distinct alterations in pre-mRNA splicing. It is therefore unclear if such mutual exclusivity is due to overlapping biological effects and/or synthetic lethal interactions. Furthermore, although cells bearing mutant splicing factors have been shown to require the wildtype allele for survival, whether these mutations can exist in a homozygous state is unknown. Here we addressed these questions by analyzing the effects of expressing SF3B1 and SRSF2 mutations simultaneously or in a homozygous state in vivo. Re-analysis of published sequencing data revealed that only 2% of MDS patients (86/4,032) have mutations in >1 splicing factor simultaneously (whether these mutations are present in the same cell or not is unclear). Of these 86 patients, co-mutations in SRSF2 and SF3B1 represent the most prevalent combination (n=23/86) with all SRSF2 mutations affecting the P95 residue while all co-existing SF3B1 mutations occurred outside of the most commonly mutated K700 residue. To understand the basis for exclusivity of SRSF2P95 and SF3B1K700 mutations, we generated mice for inducible heterozygous expression of Sf3b1K700E/+ and Srsf2P95H/+ mutations simultaneously (Mx1-cre Sf3b1K700E/+/Srsf2P95H/+). We next performed competitive bone marrow transplantation (BMT) assays where each mutation was induced, alone or together, following stable engraftment (Figure 1A). Simultaneous expression of Sf3b1K700E and Srsf2P95H mutations resulted in severe defects on the self-renewal and differentiation of hematopoietic stem and progenitor cells (HSPC), which were outcompeted by wildtype and single-mutant HSPCs (Figure 1B). In noncompetitive BMT assays, HSPCs co-expressing Sf3b1K700E and Srsf2P95H mutations had severe defects in multi-lineage reconstitution (Figure 1C). Analyses of hematopoietic organs 6 months post-BMT revealed a near complete absence of Sf3b1K700E/+/Srsf2P95H/+ double-mutant cells, which was distinct from expression of Sf3b1K700E or Srsf2P95H mutationalone. In addition, mice with conditional homozygous expression of the SRSF2P95H mutation (Mx1-cre Srsf2P95H/P95H) had severe defects in HSPC self-renewal as well as multi-lineage reconstitution, analogous to those seen with hemizygous Srsf2P95H expression (Mx1-cre Srsf2P95H/KO) (Figure 1D). As noted earlier, SF3B1 and SRSF2 mutations cause different effects on mRNA splicing. However, there has never been a direct comparison of the effects of each of these mutations in an isogenic context. To address this and to understand the mechanistic basis for exclusivity of these mutations, we performed RNA-seq on lineage- c-Kit+ cells from Mx1-cre Sf3b1K700E/+/Srsf2P95H/+ andcontrols 2 weeks after conditionally expressing each mutation alone or together. As evidence of the intolerability of combined SF3B1/SRSF2 mutations, mean allelic ratio of Sf3b1K700E and Srsf2P95H expressed in double-mutant mice was 20.7% and 33.5%, respectively, markedly lower than the near 50% expression seen in single-mutant controls. Despite this, principle component analysis of differentially spliced genes revealed distinct changes mediated by expression of Sf3b1K700E and Srsf2P95H mutations (Figure 1E). Moreover, previously described changes to alternative 3" splice site selection as well as cassette exon splicing were seen in cells bearing Sf3b1K700E and Srsf2P95H mutation, respectively, as well as in Sf3b1K700E/+/Srsf2P95H/+ double-mutantcells. These findings indicate thatspliceosomalgene mutations, despite imparting distinct alterations on gene expression and splicing, are not tolerated when co-expressed in the same cell, thus providing a basis for their strong mutual exclusivity in MDS. These data, combined with the fact that neitherhemizygousnor homozygous expression of splicing factor mutations is tolerated, further establishes the unique requirement ofspliceosomalmutant cells on the remaining function ofwildtypespliceosomecomponents. Figure 1. Figure 1. Disclosures Palacino: H3 Biomedicine Inc.: Employment. Seiler:H3 Biomedicine: Employment. Buonamici:H3 Biomedicine: Employment. Smith:H3 Biomedicine Inc.: Employment.

The discovery that mRNA splicing factors are frequently mutated in clonal blood disorders represented one of the most unexpected findings from cancer genome sequencing projects. While initial functional studies of these mutations have suggested that alterations in constitutive and alternative splicing may directly contribute to malignant hematopoiesis, they also highlighted limitations in our knowledge of how splicing factors regulate differential splicing and usage of mRNA isoforms in normal hematopoietic development. Interestingly, the splicing factor SRSF2, a member of the serine/arginine-rich (SR) protein family that regulates alternative splicing in a tissue-specific manner, is recurrently mutated only in myeloid leukemias, whereas other splicing factors are also often mutated in lymphoid leukemias and epithelial cancers. These data suggest a specific role for SRSF2 in hematopoiesis and/or myelopoiesis and previous studies have shown that Srsf2 is required for T-lymphopoiesis and hematopoietic stem and progenitor cell (HSPC) function. At the same time, SRSF2s functions in regulating splicing have been suggested to be at least partially overlapping with those of SRSF1, the founding member of the SR protein family. We therefore set out to understand the role and function of SRSF1 in normal fetal and adult hematopoiesis and to directly compare SRSF1s role in normal hematopoiesis to that of SRSF2. To understand the role of Srsf1 in adult hematopoiesis, we utilized mice for conditional deletion of 1 or 2 copies of Srsf1 or Srsf2 and performed non-competitive and competitive bone marrow transplantation (BMT) assays. BM from adult Mx1-Cre/Srsf1+/+, Mx1-Cre/Srsf1fl/+, Mx1-Cre/Srsf1fl/fl and Mx1-Cre/Srsf2fl/fl mice (together with the same number of wildtype CD45.1 marrow in competitive BMT) were transplanted into lethally irradiated CD45.1 recipients, followed by polyinosinic:polycytidylic acid (pIpC) administration 4 weeks after reconstitution to induce Srsf1 deletion. In both competitive and non-competitive BMT, peripheral blood (PB) chimerism showed that while heterozygous deletion of Srsf1 did not affect PB chimerism, homozygous deletion of Srsf1 resulted in compromised multi-lineage reconstitution similar to homozygous Srsf2 deletion (Figure 1A). Analysis of hematopoietic organs 20 weeks post BMT revealed no contribution to hematopoiesis by Srsf1 or Srsf2 homozygous knockout cells. More specifically, the contribution of HSPC-enriched Lineage- Sca-1+ c-Kit+ (LSK) and myeloid progenitor-enriched Lineage- Sca-1- c-Kit+ (LK) fractions were significantly reduced in mice transplanted with Srsf1- and Srsf2-deficient BM (Figure 1B). These observations identify an absolute requirement for both splicing factors in HSPC function in adult mice. To determine if Srsf1 or Srsf2 are required for fetal hematopoiesis, we crossed Vav-CreTg/Srsf1fl/+ to Srsf1fl/fl mice and Vav-CreTg/Srsf2fl/+ to Srsf2fl/fl mice followed by HSPC analysis at embryonic day 13~14. At this time point, both Vav-CreTg/Srsf1fl/fl and Vav-CreTg/Srsf2fl/fl embryos were found at the approximate expected Mendelian ratio (p=0.77 for Srsf1 crosses and p=0.22 for Srsf2 crosses; Fishers exact test). Interestingly, the numbers of HSPCs and erythroid progenitors (determined by flow cytometry using Ter119 and CD71 antibodies) were similar in Vav-CreTg/Srsf1fl/fl fetal livers compared to control embryos, while Vav-CreTg/Srsf2fl/fl fetal livers had drastically reduced fetal liver cellularity, HSPC, and erythroid progenitors relative to control embryos. However, both Vav-CreTg/Srsf1fl/fl and Vav-CreTg/Srsf2fl/fl HSPCs had reduced colony-forming capacities in vitro relative to control, suggesting severe functional defects in homozygous mutants that are otherwise not observed in heterozygous mice. The above data identify that both Srsf1 and Srsf2 are essential for normal hematopoietic function in both embryonic and adult life. Although SRSF1 and SRSF2 have been suggested to regulate splicing by binding to similar sequences of pre-mRNA to promote splicing, here we find that both are absolutely required for hematopoiesis in a haplosufficient, non-overlapping manner. We are now performing transcriptomic analyses to delineate the common as well as distinct molecular targets of how SR proteins regulate HSPC function. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.

Mutations in the spliceosomal genes SRSF2, U2AF1 and SF3B1 are commonly found in patients with myeloid malignancies including myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). These mutations occur at highly restricted amino acid residues, are always heterozygous, and rarely co-occur with one another. These data suggest that splicing factor mutations confer an alteration of splicing function and/or that cells may only tolerate a certain degree of splicing modulation. Consistent with this, it has been recently shown that mice expressing the heterozygous Srsf2P95H mutation develop MDS-like features due to altered mRNA recognition. To begin to identify therapeutic vulnerabilities created by spliceosomal gene mutations, we first generated Mx1-Cre Srsf2P95H/KO mice to study the effects of wildtype Srsf2 deletion with concomitant activation of the Srsf2P95H mutant allele. In noncompetitive transplantation, hemizygous Mx1-Cre Srsf2P95H/KO mutant mice exhibited severe bone marrow failure due to complete loss of hematopoietic stem/progenitor cells (HSPCs), suggesting that Srsf2P95H cells depend on wildtype Srsf2 for survival (Fig. 1A). RNA-seq analyses revealed an increase in mis-splicing due to altered mRNA recognition in Srsf2P95H/KO hemizygous mutant HSPCs compared with heterozygous Srsf2P95H/+ mice, which resulted in strong repression of genes involved in hematopoietic self-renewal, most notably Runx1, Erg, and the entire HoxA cluster. Based on these observations, we hypothesized that spliceosomal-mutant leukemias might display greater sensitivity to pharmacologic modulation of splicing than their wildtype counterparts. To address this, we tested the efficacy of a known spliceosome modulator, E7107, in myeloid leukemias with or without splicing factor mutations in vivo. We created a murine leukemia model using MLL-AF9 overexpression on either Srsf2+/+ or Srsf2P95H/+ background, a mutational combination which represents ~10% of adult MLL-rearranged leukemias (LavallŽe et al., 2015). In vivo E7107 treatment resulted in decreased disease burden and ultimately survival benefit in Srsf2P95H/+ mice, whereas the same treatment regimen had no impact on overall survival of Srsf2+/+ mice (Fig. 1B). RNA-seq analysis of leukemic cells after 5 consecutive days ofE7107 treatment in vivo revealed massive global splicing inhibition in response to E7107 in both genotypes, most notably global cassette exon skipping and retention of both constitutive and alternative introns. E7107-induced splicing inhibition was more severe in Srsf2P95H/+ versus Srsf2+/+ mice, consistent with its differential effect on survival in these 2 genotypes. Interestingly, among the most differentially spliced genes in Srsf2P95H/+ mice in response to E7107 are genes involved in maintaining the leukemogenic programs in MLL-rearranged leukemias, including Dot1l, Meis1 and Lsd1 (Fig. 1C). To confirm that preferential sensitivity of spliceosomal-mutant myeloid leukemias to splicing modulation is directly translatable to a human context, we next generated patient-derived xenografts (PDX) from AML patients wildtype (n=2) or mutant (n=3) for splicing factors. 10 mice were successfully engrafted per patient via tail-vein injection in NSG mice and treated with vehicle or E7107 for 10 days once human bone marrow chimerism was >50%. In each PDX model, targeted genomic analysis of human leukemic cells confirmed faithful engraftment of the major leukemic clones as found in patients pre-engraftment and that spliceosomal mutations were present in the major leukemic clone engrafted in mice. All spliceosomal mutant AML PDXs showed significant reductions in human leukemic burden in response to E7107 while the response in splicing wildtype AML cells was less robust (Fig. 1D). Collectively, these data provide both genetic and pharmacologic evidence that splicing factor mutant leukemias are preferentially sensitive to splicing modulation in vivo compared with spliceosomal wildtype counterpart cells. This has important therapeutic implications for the wide range of patients with MDS and AML bearing these alterations. Figure 1. Figure 1. Disclosures Thomas: H3 Biomedicine: Employment. Buonamici:H3 Biomedicine: Employment. Smith:H3 Biomedicine Inc.: Employment.